Anthropomorphic chemicals

A quick disclaimer: this post is written entirely from the perspective of a synthetic chemist. I don’t know much about the attitudes of analytical, environmental, computational or other chemists towards their work — but I would be very interested in finding out. Check in with me in the comments!

I have noticed during my years of studying chemistry that there is an almost universal tendency between chemists to anthropomorphise chemistry. One particular example I run into often is in relation to figuring out how and why a reaction works. Synthetic chemists are concerned with reaction mechanisms: exactly what happens in a reaction to transform the starting material into the product. Reaction mechanisms usually involve several steps, and several different molecules, from the starting materials to solvents and intermediates, which are somewhere between the starting material and the product. While figuring out mechanisms with colleagues, I’ve heard chemists referring to molecules as “this guy,” as in “this guy then goes on to do that, while this guy just sits around watching the whole thing happening.” In my line of work, I’ve also heard this expression when colleagues are figuring out relationships between crystal structures. “This guy” then refers to particular crystal structure. The fascinating thing about this expression is that if it were only about simplifying communication for office chatter, we could easily have adopted a slang expression like “this thing” or variant thereof. Instead, we use a very humanising term, which implies identity and agency.

Copper doesn't want to_1There is a second example of anthropomorphising chemicals that I personally am guilty of. I work in coordination chemistry, which involves organic molecules (ligands) that we try to get to bond with metal ions. Sometimes the metal ions and ligands behave in predictable ways, but sometimes they do something entirely baffling or nothing at all. In the latter two cases, I find myself talking about how the metal ion “wants” to do something in particular — that it “likes” the solvent more than the ligand, or just “doesn’t want to” bond to two different things at once. Of course, it is entirely impossible for an atom to want to do anything in the way we as humans want to, so the expression is entirely inaccurate — and we know that. So why do we do it?

I think the beginning to the answer lies in that chemistry is even now primarily an experimental science. In crystallography, for example, it has been shown that it is still very difficult for computers to predict the intricacies of crystal structures. Growing crystals, collecting data and then solving the structure is the only reliable way to go. I’m not trying to dismiss computational chemistry — but I would think that even computational chemists agree that a combination of experimental and computational chemistry produces the most meaningful results for now.

As an experimental science, then, the best (or only) way to learn chemistry is by doing it. That can seem like a baffling statement, as though I’m claiming that mixing things willy-nilly will magically transfer in-depth knowledge of chemistry into your brain. This is sadly not possible. What I mean with learning chemistry through practice is that the more practical chemistry you do, the better you become at it. To be a successful chemist, you do have to know how the theory works so that you can intelligently select your targets, building blocks and conditions. But when it’s about a particular system that you are working on and refining, or even a particular technique, working with it over a period of time begins to give you a sense  of what will and won’t work. Tangible knowledge that you can write down or impart on the next student or researcher coming to work in your field is almost never the first result of experimentation. The first result is just an abstract feeling which makes you chase one path and abandon others.

Oxygen_1Perhaps you can see the connection forming here. The relationship between an experimental chemist and their chemistry can be sort of like a relationship between people: based strongly on intuition and instinct. I am sure many of us have met a person we have either liked or disliked for a reason that isn’t entirely obvious to us from the get-go. That is the same sort of level of feeling I’m talking about in the realm of chemistry. I guess it’s no wonder, then, that many of us resort to anthropomorphising terms when describing our chemistry, when human interaction is the realm we’re used to when dealing on that cognitive level.

There is a pitfall here: with anthropomorphising your work, you risk developing affection for it. The problem with that is the possible development of confirmation bias — you want your chemistry to work out, so you are more likely to interpret ambiguous data as a success rather than a failure. That is a whole can of ethics-related worms, though, and in the interest of brevity, I’ll leave it for another time.

My thoughts on the tendency to anthropomorphise aspects of our work is that it reflects the way chemists may think about chemistry. Although we are scientists who require hard data to support our claims, I feel that is rarely our first point of call in practical chemistry. The instinct comes first, and the data to support or debunk it comes after — which then feeds back into the subconscious knowledge of your work.

If you have feelings about this blog post, you can reach me in the comments, via e-mail at chemistryintersection@gmail.com or on Twitter, where I tweet as @Lady_Beaker.

 

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Chemistry picture of the week: Filtering

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In Australia, apart from the final talk of a PhD and obviously thesis submission, the most important event of one’s postgraduate degree is the first year confirmation. The confirmation occurs at the end of your first year, and is essentially a review of your work by your supervisor and a panel of other academics in the school. The academics’ job is to decide whether you’re suitable to be confirmed as a PhD candidate and to continue your research at the university. At the university I completed my undergraduate and honours, this was largely a formality — even the laziest of students always passed their confirmations and were allowed to continue. At the University of Melbourne, I have heard of students failing and having to resubmit. At the start of 2015, I saw two of my co-workers stressing out over their confirmations. Their nervousness was obvious — I even caught them practicing their talks in an isolated instrument room at the back of the lab. And this year, it’s my turn.

I’m a fairly fast writer once I get on a roll, so I’m not too concerned about the 30-odd pages we’re supposed to produce as the written report. I think if I leave that for the month of February, I’ll still have plenty of time — especially as I try to be organised with my data as I’ve talked about before. What I am currently concerned with is amassing as much hard data for my report as I can — so when I make a statement about my chemistry, I can refer to an experiment or measurement I’ve conducted to try to qualify or quantify that statement. As such, the last couple of weeks of December and the first weeks of 2016 have been largely spent avoiding attempts to synthesise new materials, instead repeating old reactions to yield plenty of material to conduct measurements and further experiments on. That means that my last month or so of work has consisted of a lot of filtering.

Most chemical reactions synthetic chemists perform are done in a solvent, which is a liquid such as water or ethanol that dissolves other chemicals. In many cases, the desired product is a solid, which means that you require a method to separate the solid from the remaining liquid. Enter filtering. Filtering may be familiar from filter coffee, which is made by passing boiling water through a filter paper holding coffee grounds. The end result is the extract of coffee without the solid coffee beans. Filtering works in the reverse: you start with a mixture of solid and liquid, and pass the mixture through a filter paper which catches the solid and deposits the liquid. To speed up the process, we use vacuum filtering, which pulls the liquid through much faster and also dries the remaining solid.

Here’s a secret, though: it’s deathly boring, particularly when you’re filtering tiny amounts and are trying to make sure you don’t lose any of your product. When it’s small crystals, you want to drop as much solid at a time onto the filter paper and always drop it on the same, small spot so that the solid can catch more solid. It’s a slow, painstaking process when you have vials and vials and vials to empty using this method. Afterward, I do get to look at my beautiful shiny crystals under the microscope to note the appearance of the bulk product, which does give a bit of satisfaction to the whole process. In the worst case scenario (which happens frustratingly often given how science tends to require a lot of trial and error), I end up wasting this little bit of product on an experiment that gives me no useful results, and I have to remake the material — which means filtering time is again upon me.

Amassing useful results for my confirmation report is difficult work, but it is immensely rewarding to watch the troves of data gathering and forming the beginnings of an interesting “story.” Every little piece gives me more insight into how my system works, and I really do love that. That sense of satisfaction is what makes it worth doing the repetitive, sometimes frustrating tasks it takes to get there.

For comments or queries, you can reach me at chemistryintersection@gmail.com, in the comments or on Twitter as @Lady_Beaker, where I tweet about the everyday happenings of my PhD.

Chemistry PhD resolution for 2016

As the year is starting up, I — like most everyone — reflect back on the past year and consider my hopes and expectations for the future.

For me, last year began with great motivation and enthusiasm toward my new group and project. The year then descended into predictable frustration and self-doubt when results weren’t instant and easy. About four months in, I finally made my breakthrough, but my progress was greatly impeded by the fog of exhaustion and disorientation brought on by my extended illness. Despite this, I managed to push through and have a handful of interesting results to elaborate on. This work is not nearly finished, which is beginning to worry me — my supervisor told me halfway through the year that he would love for me to have this thesis chapter done and dusted by March-April 2016. Additionally, the self-doubt intensified by my illness still lurks at the back of my mind. For the last few months of 2015, I was not sure whether I was simply lazy or still recovering, but I never felt as though I was working the hardest I possibly could.

During the year, I have become at home in my new group — there are several group members I can now confidently call good friends. I’m slowly making myself familiar to the academic staff in the building through demonstrating, seminars, social events and such. I have joined the Royal Australian Chemical Institute (RACI) as a student member, as well as the Australian Science Communicators. I attended a few events organised by the former over the course of the year, although mostly only to catch up with co-workers from my old university.

This is where I stand. When thinking about New Year’s resolutions, I don’t like to make extensive lists. I feel as though the greater the number of goals, the greater the chance of failure — and the greater the number of failures, the easier it is to simply give up. Instead, I like to think of a few important things I would like to keep in the back of my mind as I start the new year. Habits take time to make and change, so I like to give myself some wiggle-room. On this track, I started thinking of a few things I would like to focus on in the coming year. I thought perhaps I should give myself a single goal in the categories of academia that are important to me right now: my research, networking, teaching and communicating. The more I thought about it, however, the clearer it became that all of those goals could be smushed into a single idea, which is the following:

Push your boundaries.

It is so easy to do what is comfortable and familiar. Continuing on a track of your research that is perhaps boring or bordering on stamp-collecting, but will most likely produce results. Using advice or suggestions your supervisor or co-workers have made without exploring on your own. Not attending large social events because meeting several new people in a new environment makes you feel uncomfortable. Shying away from pushing  — or even asking — for a publication with a supervisor who might be more focused on students further along in their studies than you. Neglecting to take opportunities to engage with undergraduate students because you aren’t sure you’re the best person for the job. Neglecting to take on larger challenges in addition to your research because you’re afraid of how much of your free time it’ll consume. Arriving late to work because getting out of bed in the morning is one of the hardest little things to do for an evening person.

These are just a few things where pushing myself to do the slightly uncomfortable thing will greatly benefit me. It has been a mentality I have tried to cultivate even throughout 2015, but this year, I want to push even harder. Some decisions I will regret, I am sure, but as the saying goes — what doesn’t kill you only makes you stronger.

If you’d like to share what your resolutions for 2016 are, you can find me in the comments, by e-mail at chemistryintersection@gmail.com or on Twitter as @Lady_Beaker, where I tweet about the daily life of a PhD student in chemistry.

Chemistry picture of the week: Organising information

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This is a picture of my real experimental books and the folder I file my spectra in. I have blurred out the text for privacy’s sake — all of my work is unpublished so far, and plastering it all over the internet seems to be a terribly bad idea.

The experimental notebook is a researcher’s most important tool. This is the book we use to record all the facts about our research. In chemistry, that usually involves identities and quantities of chemicals used, time the reaction was heated or stirred and similar sort of details that are crucial to reproducing a result. Reproducibility is, after all, one of the main requirements of science.

Arguably, the experimental book is also the most difficult resource to keep organised, as I’ve talked about before. One method to keep on top of one’s results is to transcribe important features of experiments  into an Excel spreadsheet. For my project, which is currently centered around one material only, a useful organisation method is a “conditions attempted” spreadsheet where I outline the variables changed for each reaction.  Although very thorough, this method has the disadvantage of being time-consuming. Writing the same thing down twice can feel like a colossal waste of time. I can only hope that when it comes to writing my first year confirmation report (yikes!) or even my thesis, having a neat document that displays the “bigger picture” of my work will be useful.

For systems that I have found to work time and time again, I build a separate spreadsheet that keeps track of all the analyses I have performed on that particular system. For publication and one’s thesis, a number of different analyses are important, as I’ve mentioned before. A spreadsheet like this is a straight-forward way to show what data I have and what is missing. Linking the spreadsheet entry to the corresponding data is also a neat way of keeping your files organised.

These spreadsheets are wonderful for having an eagle’s eye view of your research — taking a step back from the messy world of your experimental book. Still, making these spreadsheets requires an easy way to find information in your lab book itself. A universally accepted method of keeping your experimental book organised is to have a consistent reaction numbering system.  In my Honours year, I used a method wherein each reaction was numbered. Toward the end of that year, however, I found that the reaction numbers might occasionally become jumbled in my book and finding the information for a particular one could be annoying, if not difficult. This year, I have elected instead to use the page number method: each reaction is labeled by my initials, followed by the book number, then page number, then a letter if there are multiple reactions on one page. This makes particular reactions extremely easy to find — simply find the correct book and turn to the page indicated.

For further information about particular reactions, I use highlighters. I write fairly comprehensive notes, and often have to go back to old reaction notes to write new observations (crystal growth or lack thereof, new analyses — that sort of thing). The result of these two things is that my pages can get very cramped. Small, but perhaps important notes can then be missed at a glance. Hence, the highlighters. I use yellow as an indicator for a type of analysis (or postsynthetic modification — further reactions on a material) conducted on the product of a reaction. Green is for reactions which were suitable for crystallography. Orange is for overarching observations — often something I have seen systematically through several reactions and have come to conclude about that system in general. This colour coding is very helpful when it comes to looking at past reactions and thoughts I may have had about them that I might otherwise have forgotten or missed.

There you have it: two ways to keep your data organised, and two ways of keeping your experimental book organised. If you would like to share how you organise your data, you can find me in the comments, on Twitter as @Lady_Beaker or by e-mail at chemistryintersection@gmail.com

Chemistry picture of the week: Buggy research

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When I talk about bugs in my research, I wish I was talking about software or something. No, the problem we are currently experiencing in my lab is more literal than that.

A couple of weeks ago, I and coworkers in the same section of the lab noticed these black particulates accumulating on our lab bench. We shrugged it off for a week or so, but it soon became a real annoyance. Having to brush little black things off of your precious clean vials, or, worse, having to pick them out from a product you filtered the day before can be, if not detrimental, then irritating at the very least. We observed that the black things were confined to below the large air conditioning vent above our lab benches. We notified the building manager about it. He expressed concern over the situation, saying that it could mean that there is something wrong with the air conditioning. He would have someone look at it.

I turn up to work on the next day, having missed the air conditioning technician who came by earlier that morning. A coworker accosts me: “Hey, have you looked at those black things? Like… really looked at them?” His tone is mischievous and ominous and I’m really not a fan of it. The air conditioning technician had identified the black stuff as thrips — tiny insects that are killed in the air conditioning system but are too small for the filters. As a consequence, our work benches were being rained on by tiny dead insects. I don’t think I really need to qualify that declaration with a record of my reaction. I think that statement — “rain of dead insects” — is graphic enough on its own.

I have to give it to my university: they were very prompt at identifying the issue. The building manager even followed up with the information that Campus Services has agreed to upgrade the filters to stop it.

We are still dealing with the rain of dead bugs, but hopefully not for long — especially since we have recently spotted a few live ones crawling around. And I swear… They’re getting bigger.

You can reach me in the comments, by e-mail on chemistryintersection@gmail.com or on Twitter, where I tweet about daily science happenings as @Lady_Beaker.

 

Advice for new PhD students

Do not contract glandular fever in your first year. It’ll put a real damper on your studies.

I never really got any better after those few illnesses I complained about earlier this year. I was really sick about every second week, and when I wasn’t actively bedridden, I had only just enough energy to push myself through the daily grind. Extra things like seeing my friends or writing on this blog and other hobbies just had to drop.

Even after finishing a demanding Bachelor’s degree and a hectic Honours year, I can say that I have never felt that exhausted in my life. I saw a doctor several times. When things still weren’t getting better after I “recovered” from one of my endless colds, I had some blood tests done. Everything came back negative. I cried at the doctor in frustration. I felt horrible, and I didn’t know why.

With this persistent exhaustion and illness came crippling self-doubt. Maybe there is really nothing wrong with me, maybe I’m just not cut out to do a PhD. All my co-workers are putting in more hours than me, working harder than me, and they’re not as tired as I am. Maybe I made the wrong choice. Maybe I should quit.

I finally took two solid weeks off on advice from that doctor who still didn’t know what was wrong with me but probably thought some rest wouldn’t hurt. Asking for that time off, I cried at my supervisor. Thankfully, he was extremely kind and understanding — the second week was actually his idea, I originally only asked for one.

When I returned from my time off, I saw a different doctor to fill a prescription, and although I felt much better at the time, I filled her in on the situation. She thought to test for glandular fever. I just received the results today, and the diagnosis is that I have had it. Although it has been obvious to me that I’m now better, given my higher energy levels and lack of very recent illness, somehow I feel better for having that diagnosis. I guess I feel validated for all that time I had to take off to be a pathetic lump in bed or on the couch. It wasn’t just in my head.

I definitely feel like things are going to pick up from here. My research is doing very well; I think I am getting useful results almost every day now. That sort of thing is possible when you crack the synthesis of a material — I’m now in the process of testing it for all the different sorts of things it can do. Hopefully my personal life will also lift back up again and I can get back to regular posting. I am certainly going to try.

If you wish to talk, you can find me in the comments, via e-mail at chemistryintersection@gmail.com or on Twitter as @Lady_Beaker.

Chemistry picture of the week: Fibre hunting

In an unfortunate series of coincidences, my last post appears to have been prophetic, regarding my partner’s cold, which I mentioned in passing. Where the prophecy lied was the nature of the disease — it turned out to be a monster flu that absolutely wiped me out for two weeks. At best, even standing was too much effort for me for the past couple of weeks. But finally, the illness is over and I can return to business as usual. That business, of course, is crystals.
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As you may have read in the guest post I wrote for #RealTimeCheminFocus, I recently had a breakthrough in my project — in the sense that I finally found a way to synthesise the material I had been aiming for all year. I have since been experimenting with a number of synthetic variables to see how many different variations of this material I can make, and how its structure and properties can vary. The material is a coordination polymer, which is an “infinitely” repeating assembly of metal ions and organic ligands. My ultimate aim is to take these compounds through postsynthetic modification — simply, chemical reactions of the coordination polymer to give different properties. In order to do this, I have been working on characterising my compounds so that I can tell how they change once I put them through these experiments.

Today, I was preparing samples to send to an analytical laboratory for elemental analysis. Elemental analysis involves breaking down a compound to its elemental components in order to give a percentage composition of the compound, most often in terms of carbon, hydrogen and nitrogen. Other elements can also be analysed for, but often require more sample, and are more expensive than a “basic” CHN analysis. In most cases, especially if other forms of characterisation are possible, analysis for anything other than these three elements is unnecessary. If a compound contains an impurity that does not contain carbon, hydrogen or nitrogen, it can still be seen in the elemental analysis by proxy, since the impurity will affect the overall percentage composition. Elemental analysis is excellent for determining the exact amount of counter-ions and solvent in coordination polymers, where these variables can be unclear.

For elemental analysis results to be usable, it is critical that the samples I send are as pure and clean as possible. Crystalline samples are preferred, since the composition of a crystal is uniform. Coordination polymers are almost always formed through crystallisation from a reaction mixture, so all that remains is to collect the crystals, wash them of possible soluble impurities and then dry them. In my group, there is also a practice of checking the quality of the sample under a microscope prior to packaging it for elemental analysis. Painstakingly sifting through piles and piles of cubic crystals using a small needle, I found a surprising number of fibres of confusing origin, pieces of glass and other assorted debris. Of course, there is no way to tell by eye whether the sample is truly pure or not, which is why we need this analysis in the first place, but removal of this visible debris can only help make the analysis results more helpful for accurate composition determination.

Besides, looking at the piles of shiny, beautiful crystals that I strived so hard for so long to make fills me with great joy. Just being able to pack up enough material for analysis is a great victory in my book. Let’s just hope that victory doesn’t turn into defeat in confusion once I receive the results.

I am available for correspondence through the comments, and via e-mail at chemistryintersection@gmail.com. You can also find me tweeting away as @Lady_Beaker.